moved utilities out of mothur.h and into mothurOut class.

[mothur.git] / formatcolumn.cpp

diff --git a/formatcolumn.cpp b/formatcolumn.cpp
index 64b85317d1303658627f4ed6cfde1f99b51d3677..2bbcf518b864aa5a5656a271f2922c531e74af11 100644 (file)
--- a/formatcolumn.cpp
+++ b/formatcolumn.cpp
@@ -12,7 +12,7 @@
 
 /***********************************************************************/
 FormatColumnMatrix::FormatColumnMatrix(string df) : filename(df){
-       openInputFile(filename, fileHandle);
+       m->openInputFile(filename, fileHandle);
 }
 /***********************************************************************/
 
@@ -35,7 +35,7 @@ int FormatColumnMatrix::read(NameAssignment* nameMap){
                
                ofstream out;
                string tempOutFile = filename + ".temp";
-               openOutputFile(tempOutFile, out);
+               m->openOutputFile(tempOutFile, out);
        
                while(fileHandle && lt == 1){  //let's assume it's a triangular matrix...
                
@@ -68,7 +68,7 @@ int FormatColumnMatrix::read(NameAssignment* nameMap){
                                
                                reading->update(itA->second * nseqs / 2);
                        }
-                       gobble(fileHandle);
+                       m->gobble(fileHandle);
                }
                out.close();
                fileHandle.close();
@@ -79,7 +79,7 @@ int FormatColumnMatrix::read(NameAssignment* nameMap){
                }else{ squareFile = tempOutFile; }
                
                //sort file by first column so the distances for each row are together
-               string outfile = getRootName(squareFile) + "sorted.dist.temp";
+               string outfile = m->getRootName(squareFile) + "sorted.dist.temp";
                
                //use the unix sort 
                #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
@@ -94,10 +94,10 @@ int FormatColumnMatrix::read(NameAssignment* nameMap){
 
                //output to new file distance for each row and save positions in file where new row begins
                ifstream in;
-               openInputFile(outfile, in);
+               m->openInputFile(outfile, in);
                
                distFile = outfile + ".rowFormatted";
-               openOutputFile(distFile, out);
+               m->openOutputFile(distFile, out);
                
                rowPos.resize(nseqs, -1);
                int currentRow;
@@ -117,7 +117,7 @@ int FormatColumnMatrix::read(NameAssignment* nameMap){
                        
                        if (m->control_pressed) { in.close(); out.close(); remove(distFile.c_str()); remove(tempOutFile.c_str()); remove(outfile.c_str()); delete reading; return 0; }
                        
-                       in >> first >> second >> dist; gobble(in);
+                       in >> first >> second >> dist; m->gobble(in);
                        
                        if (first != currentRow) {
                                //save position in file of each new row